Impact of GC content on gene expression pattern in chicken.
Impact of GC content on gene expression pattern in chicken.
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DOI：
10.1186/1297-9686-45-9
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发表时间：
2013-04-04
期刊：
影响因子：
--
通讯作者：
Zhang XQ
中科院分区：
文献类型：
--
作者：
Rao YS;Chai XW;Wang ZF;Nie QH;Zhang XQ
GC含量在许多真核生物的不同基因组区域之间变化很大。为了确定这种称为等容线组织的组织是否影响基因表达模式，在人和小鼠中研究了GC含量和基因表达之间的关系。然而，到目前为止，这个问题仍然是一个有争议的问题。在鸟类中，鸡（Gallus gallus）是研究最多的代表，拥有完整的基因组序列。其序列的独特特征和组织使其成为探索基因组结构和进化中重要问题的良好模型。本研究仅包括具有蛋白质编码序列完整信息且无多重剪接形式证据的核基因。从Ensembl下载鸡蛋白编码序列、完整mRNA序列（或全长cDNA序列）和5′非翻译区序列（5′ UTR），鸡表达数据来自先前的工作。用表达水平、表达宽度和最大表达水平三个指标来衡量给定基因的表达模式。使用UCSC基因组浏览器的hgTables鉴定CpG岛。变量之间的相关性分析采用SAS专有软件8.1版进行。在鸡中，5′ UTR的GC含量与表达量、表达宽度和最大表达量呈显著正相关，而编码序列、内含子和第3编码位的GC含量与表达量和表达宽度呈负相关，与最大表达量无关。这些显著趋势与重组率、染色体大小和基因密度无关。此外，多元线性回归分析表明，基因中的GC含量可以解释约10%的基因表达变异。GC含量与基因表达模式密切相关，可能是鸡基因组中重要的调控因子之一。
GC content varies greatly between different genomic regions in many eukaryotes. In order to determine whether this organization named isochore organization influences gene expression patterns, the relationship between GC content and gene expression has been investigated in man and mouse. However, to date, this question is still a matter for debate. Among the avian species, chicken (Gallus gallus) is the best studied representative with a complete genome sequence. The distinctive features and organization of its sequence make it a good model to explore important issues in genome structure and evolution. Only nuclear genes with complete information on protein-coding sequence with no evidence of multiple-splicing forms were included in this study. Chicken protein coding sequences, complete mRNA sequences (or full length cDNA sequences), and 5′ untranslated region sequences (5′ UTR) were downloaded from Ensembl and chicken expression data originated from a previous work. Three indices i.e. expression level, expression breadth and maximum expression level were used to measure the expression pattern of a given gene. CpG islands were identified using hgTables of the UCSC Genome Browser. Correlation analysis between variables was performed by SAS Proprietary Software Release 8.1. In chicken, the GC content of 5′ UTR is significantly and positively correlated with expression level, expression breadth, and maximum expression level, whereas that of coding sequences and introns and at the third coding position are negatively correlated with expression level and expression breadth, and not correlated with maximum expression level. These significant trends are independent of recombination rate, chromosome size and gene density. Furthermore, multiple linear regression analysis indicated that GC content in genes could explain approximately 10% of the variation in gene expression. GC content is significantly associated with gene expression pattern and could be one of the important regulation factors in the chicken genome.
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影响因子：
3.5
作者：
Pesole, G;Mignone, F;Liuni, S
通讯作者：
Liuni, S
DOI：
10.1016/j.bbrc.2007.12.155
发表时间：
2008-03-14
影响因子：
3.1
作者：
Arhondakis, Stiliano's;Clay, Oliver;Bernardi, Giorgio
通讯作者：
Bernardi, Giorgio
影响因子：
14.9
作者：
Vinogradov, AE
通讯作者：
Vinogradov, AE
影响因子：
11.4
作者：
Vinogradov, AE
通讯作者：
Vinogradov, AE
影响因子：
12.3
作者：
Mignone F;Gissi C;Liuni S;Pesole G
通讯作者：
Pesole G